title: pol32D BrdU 25C 30' MNase add S.pombe spike in rep1 [Alb840_pol32D_BrdU_S30]

description: add S.pombe spike in


title: SUM159PT cells_sorted for TM4SF1_high and propagated for four passages_replicate1

status: Public on May 31 2024

type: SRA

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

library_source: transcriptomic

data_processing:
HTS-FLOW v2
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to hg38  using STAR
Read count extraction and TPM normalization were performed using FeatureCounts; DEGs were called using EdgeR within Galaxy (Galaxy Version 3.36,0)
Assembly: hg38
Supplementary files format and content: TM4SF1_GEX_counts.txt: tab delimited file that includes raw count values for all genes (Sorted samples: input of EdgeR)
Supplementary files format and content: edgeR_TM4SF1_high-BULK.tsv: EdgeR output files containing L2FC and FDR for TM4SF1 high vs bulk samples at Sorting
Supplementary files format and content: TPM_counts.txt: tab delimited file that includes TPM for all genes in all samples (Sort, P4, P19)

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was harvested using Maxwell RSC miRNA Tissue Kit according to the manufacturer’s protocol.. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq Total RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: SUM159 were stained with an anti-TM4SF1-APC antibody (miltenyi) and sorted using Fusion Aria Sorter. The top 5% TM4SF1 cells were gated as "high".

tag: cell line

tag: tissue

value: breast

tag: Sex

value: female

tag: time

tag: treatment

value: untreated


title: SUM159PT cells_bulk sorted_replicate3


title: BMMCs, si12A+C, 2

type: RNA

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

description: NanoString nCounter Myeloid Innate Immunity Panel

hyb_protocol: Samples were hybridized for 16h at 65°C

scan_protocol: Samples were ran on a Nanostring Sprint Profiler

data_processing: Raw data was filtered for genes with counts value of >50 and processed with batch correction using the Omics Playground platform.

label: not provided

organism: Mus musculus

source_name: BMMCs transfected with siRNAs against Zc3h12a and Zc3h12c, stimulated with IgE-antigen complexes for 2h

label_protocol: 50ng of total RNA were labelled with the nCounter Myeloid Innate Immunity Panel codeset according to manufacturers protocol

growth_protocol: Total bone marrow was isolated from mouse and cultured in humidified atmosphere with 5% CO2 at 37C for at least 4 weeks in the presence of IL-3 to induce bone marrow-derived mast cell (BMMC) differentiation. BMMCs were transfected with siRNAs and cultured for 48 hours.

extract_protocol: Cells were resuspended in Trizol and total RNA was extracted with Direct-Zol RNA mini Prep (Zymo Research)

treatment_protocol: Cells were activated IgE and antigen complexes for 2h.

tag: cell type

value: bone marrow-derived mast cells

value: 2h IgE-antigen stimulation

tag: sirna-targeted gene/s

value: Zc3h12a and Zc3h12c

tag: sample type

value: test


title: p21_ms_tim1

city: Boston

first: Shannan

last: Ho Sui

address: 401 Park Drive

country: USA

institute: Harvard

data_processing:
bcbio-nextgen bulk RNA-seq pipeline (version 1.2.8-1c563f1)
Assembly: hg38
Supplementary files format and content: TPM counts from Salmon aggregated at the gene level by tximport

source_name: Peripheral blood

extract_protocol:
Trombetta Protocol
Nextera XT

value: Peripheral blood

value: TIM-1+ memory B (TIM-1+ TIGIT-) cells

tag: patient


title: BMMCs, si12C, 2

source_name: BMMCs transfected with siRNAs against Zc3h12c, stimulated with IgE-antigen complexes for 2h


title: BMMCs, si12A, 2

source_name: BMMCs transfected with siRNAs against Zc3h12a, stimulated with IgE-antigen complexes for 2h


title: BMMCs, siGLO, 2

source_name: BMMCs transfected with non-targeting siGLO, stimulated with IgE-antigen complexes for 2h

value: control


title: p18_ms_tim1


title: pol3pip Input 25C 30' sonication add S.pombe spike in rep1 [Alb829_pol3pip_Input_S30]

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

description: add S.pombe spike in

library_source: genomic

data_processing:
Raw reads were firstly trimmed by Cutadapt (Marcel, 2011) to remove adapters and low quality reads, and then mapped to the yeast genome (sacCer3) using Bowtie2 (Langmead and Salzberg, 2012).Duplicate reads were further filtered by Sambamba (Tarasov et al., 2015) to remove PCR duplication.
The genome-wide read coverage on Watson and Crick strands were calculated at the bin of 1bp using deepTools bamCoverage (Ramirez et al., 2016). Then, the raw genome-wide read coverage was normalized with the number of total mapped reads to obtain counts per million value (CPM).
Spike-in added samples normalization. For each Sonication-BrdU-IP-ssSeq sample, the raw genome-wide coverage was normalized using the formula: BrdUsoni = (BrdUcov / BrdUspike) / (Inputread / Inputspike). BrdUcov is the raw coverage of BrdU-IP-ssSeq; BrdUspike is the number of total mapped spike-in reads (S. pombe reads) in BrdU sample, Inputread is the number of total mapped reads in input, and Inputspike is the number of total mapped spike-in reads (S. pombe) in input. In this way, BrdU incorporation at each strain was quantified as BrdUsoni.
Spike in added samples normalization. For each MNase-BrdU-IP-ssSeq dataset, reads with the nucleosome sized (120~170bp) were first selected to calculate the raw coverage of nucleosome occupancy surrounding replication origins, and then normalized using the formula: BrdUMNase = (BrdUcov-MNase / BrdUspike-MNase) / (Inputread-MNase / Inputspike-MNase). BrdUcov-MNase is the raw coverage of the nucleosome-sized reads, BrdUspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same sample, Inputread-MNase is the number of mapped  nucleosome-sized reads in input, and Inputspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same input sample. In this way, the nucleosome occupancy on nascent chromatin was quantified as BrdUMNase.
Assembly: saccer3
Supplementary files format and content: tar of bw, bigwig format, CPM which is normalized by total number of reads
Supplementary files format and content: tar of bw, bigwig format, BrdU coverage normalized by spike-in and input described as formulas above.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: For most experiments, yeast cells were cultured and synchronized at G1 phase following standard procedures (Dunham et al., 2015). ChIP, BrdU-IP-ssSeq, and eSPAN sample collection was performed as described previously (Gan et al., 2017; Yu et al., 2018). Briefly, exponentially growing yeast cultures at OD600=0.4-0.5 were synchronized by adding a-factor at 5mg/ml and arrested for 3h at 25°C.

extract_protocol:
For analysis of DNA replication by BrdU-IP-ssSeq, and PCNA ChIP and eSPAN experiments, chromatin was fragmented by sonication (15 seconds on and 30 seconds off for 10 cycles in a Bioruptor Pico, Diagenode). For analysis of nucleosome occupancy at nascent chromatin, H3K4me3 and H3K56ac ChIP as well as almost all eSPAN experiments except those marked by sonication, chromatin was digested with MNase to map nucleosomes (Wal and Pugh, 2012).
The ssDNA libraries were prepared using the Accel-NGS 1S Plus kit (Cat no. 10096, Swift Bioscience).

treatment_protocol: Cells were then released into fresh YPD medium containing 400mg/ml BrdU without HU for 30 or 40 minutes at 25°C. For experiments using auxin-inducible protein degradation mutant strains, 1mM IAA or the equivalent volume of ethanol was added to the arresting culture (30 minutes before release) and cells were released in YPD medium also containing IAA or ethanol.

tag: batch

tag: strain

tag: condition

value: 25C 30' sonication

tag: genotype

value: Input


title: pol32D Input 25C 30' MNase add S.pombe spike in rep2 [Alb890_pol32D_Input_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: SUM159PT cells_bulk sorted and propagated for four passages_replicate1


title: pol3pip BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb904_pol3pip_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: SUM159PT cells_bulk sorted_replicate1


title: SUM159PT cells sorted for TM4SF1_high_replicate3


title: p22_ms_tim1


title: BMMCs, si12A+C, 1


title: p15_ms_tim1


title: p24_hc_tim1


title: pol3pip BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb841_pol3pip_BrdU_S30]

description: add S.pombe spike in


title: pol3pip Input 25C 30' MNase add S.pombe spike in rep2 [Alb892_pol3pip_Input_S30]

description: add S.pombe spike in


title: p14_ms_tim1


title: pol3pip Input 25C 30' sonication add S.pombe spike in rep2 [Alb891_pol3pip_Input_S30]

description: add S.pombe spike in


title: BMMCs, si12C, 1


title: SUM159PT cells sorted for TM4SF1_high_replicate1


title: BMMCs, si12A, 1


title: SUM159PT cells_bulk sorted_replicate2


title: p9_ms_tim1


title: BMMCs, siGLO, 1


title: in vivo, replicate 6, PTX, targeted DNA-Seq

description: in vivo

data_processing:
Genetic barcode libraries were generated using seqkit v2.1.0 and error correction was performed with in-house scripts.
Supplementary files format and content: Tab-separated value files
Library strategy: DNA-Seq

source_name: breast

extract_protocol:
The genomic DNA was extracted from at least one million cells using the NucleoSpin Tissue kit (Macherey-Nagel).
GBCs were enriched from genomic DNA (1.2 ug) by PCR, using PhusionTM High-Fidelity DNA Polymerase and primers designed to capture GBC flanking regions. Amplified DNA was run on a 2% agarose gel and the 280bp band purified using the QIAquick Gel extraction kit (QIAGEN

value: Breast epithelial cell

value: paclitaxel


title: pol3pip BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb907_pol3pip_BrdU_S30]

description: add S.pombe spike in


title: p29_hc_tim1


title: ∆srtA∆ebpABC∆htrA, exponential, repl 3 (2)

city: Genève

first: Kimberly

last: Kline

address: 1 Rue Michel Servet

institute: University of Geneva

description: dSrtASdEbpdHtrA = ∆srtA∆ebpABC∆htrA

data_processing:
Sequencing reads (Accession numbers CP002621.1) mapping to predicted open reading frames (ORFs) were quantified using HTSeq
Counts for ribosomal and transfer RNA sequences were filtered out of the data set and differential expression analyses were performed in R (version 2.15.1) using the Bioconductor package, edgeR
Significantly differentially expressed genes were determined using a P-value and false discovery rate (FDR) cut-off of 0.05.
We annotated differentially expressed genes using a combination of KEGG annotations, as well as manual annotation using operon and other functional data from the literature and E. faecalis OG1RF database available on BioCyc
Assembly: RNA sequencing reads were mapped to the E. faecalis OG1RF reference genome (NCBI accession: NC_017316.1) using BWA-MEM2 (2.2.1) with default parameters
Supplementary files format and content: tab-delimited text file includes gene locus identification, log2-fold change, logCPM, and p-value and FDR for each strain/condition, as well as gene name and annotation if applicable.

organism: Enterococcus faecalis

source_name: planktonic bacteria

growth_protocol: Strains WT, ∆srtA∆htrA, and ∆srtA∆ebpABC∆htrA cells were grown in TSB supplemented with 0.25% glucose and incubated static at 37°C until mid-exponential growth phase (OD600 0.5).

extract_protocol:
Total RNA was extracted using the UltraClean® Microbial RNA Isolation Kit (MO BIO Laboratories Inc., Singapore). Extracted RNA samples were subjected to rigorous DNase treatment using TURBO DNA-free™ kit (Ambion®, Singapore) and purified DNA-free RNA samples were subjected to ribosomal depletion with Ribo-Zero™ Magnetic Kits (Epicentre®, Singapore), all according to manufacturer’s protocols. Quantification of RNA and DNA were performed using Qubit™ RNA Assay Kits and Qubit™ dsDNA HS Assay Kits (Invitrogen, Singapore), respectively. The integrity of RNA was analyzed by gel electrophoresis using Agilent RNA ScreenTape (Agilent Technologies, Singapore).
mRNA libraries for RNA sequencing were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, USA), the quality of the library analyzed via Bioanalyzer (Agilent, USA).

treatment_protocol: For antibiotic treated cells, WT cells were grown in BHI to mid-exponential growth phase (OD 0.4) and then treated with 1µg/ml daptomycin for 15 min.

value: OG1RF strain

value: planktonic bacteria

value: {delta}srtA{delta}ebpABC{delta}htrA

tag: growth phase

value: Exponential phase


title: ∆srtA∆ebpABC∆htrA, exponential, repl 2 (2)

description: dSrtASdEbpdHtrA = ∆srtA∆ebpABC∆htrA


title: p23_hc_tim1


title: pol3pip BrdU 25C 30' MNase add S.pombe spike in rep1 [Alb842_pol3pip_BrdU_S30]

description: add S.pombe spike in


title: p1_ms_tim1


title: ∆srtA∆ebpABC∆htrA, exponential, repl 1 (2)

description: dSrtASdEbpdHtrA = ∆srtA∆ebpABC∆htrA


title: WT input 25C 30' sonication add S.pombe spike in rep5 [Alb1035_WT_input_S30]

description: add S.pombe spike in

value: WT

value: input


title: in vivo, replicate 4, PTX, targeted DNA-Seq

description: in vivo

value: breast

value: female


title: in vivo, replicate 3, PTX, targeted DNA-Seq

description: in vivo


title: ∆srtA∆htrA, exponential, repl 3 (2)

description: dSrtAdHtrA  = ∆srtA∆htrA

value: {delta}srtA{delta}htrA


title: in vivo, replicate 5, PTX, targeted DNA-Seq

description: in vivo


title: p59_ms_tigit

value: Peripheral blood

value: TIGIT+ memory B (TIM-1- TIGIT+) cells


title: SUM159PT cells sorted for TM4SF1_high_replicate2

value: untreated


title: pol3pip Input 25C 30' MNase add S.pombe spike in rep1 [Alb830_pol3pip_Input_S30]

description: add S.pombe spike in

value: Input


title: ∆srtA∆htrA, exponential, repl 2 (2)

description: dSrtAdHtrA  = ∆srtA∆htrA


title: p55_ms_tigit


title: WT input 25C 30' sonication add S.pombe spike in rep4 [Alb1011_WT_input_S30]

description: add S.pombe spike in

value: 25C 30' sonication


title: WT input 25C 30' sonication add S.pombe spike in rep3 [Alb967_WT_input_S30]

description: add S.pombe spike in


title: p53_ms_tigit


title: p51_ms_tigit


title: ∆srtA∆htrA, exponential, repl 1 (2)

description: dSrtAdHtrA  = ∆srtA∆htrA


title: WT, exponential, repl 3 (2)


title: in vivo, replicate 9, targeted DNA-Seq

description: in vivo


title: WT Input 25C 30' sonication add S.pombe spike in rep2 [Alb885_WT_Input_S30]

description: add S.pombe spike in


title: in vivo, replicate 1, PTX, targeted DNA-Seq

description: in vivo


title: WT Input 25C 30' sonication add S.pombe spike in rep1 [Alb823_WT_Input_S30]

description: add S.pombe spike in


title: WT, exponential, repl 2 (2)


title: p49_ms_tigit


title: in vivo, replicate 8, targeted DNA-Seq

description: in vivo


title: WT, exponential, repl 1 (2)


title: WT BrdU 25C 30' sonication add S.pombe spike in rep5 [Alb1043_WT_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: p46_ms_tigit


title: in vivo, replicate 7, targeted DNA-Seq

description: in vivo

value: Breast epithelial cell


title: WT BrdU 25C 30' sonication add S.pombe spike in rep4 [Alb1023_WT_BrdU_S30]

description: add S.pombe spike in


title: p44_ms_tigit


title: in vivo, replicate 6, targeted DNA-Seq

description: in vivo


title: in vivo, replicate 2, PTX, targeted DNA-Seq

description: in vivo

value: paclitaxel


title: WT BrdU 25C 30' sonication add S.pombe spike in rep3 [Alb977_WT_BrdU_S30]

description: add S.pombe spike in


title: croR::tn∆srtA∆htrA, exponential, repl 3

description:
croR::tn∆srtA∆htrA 3 = 12535tndHdA_3a
croRtnsrtAhtrA vs srtAhtrA comparison.xlsx

data_processing:
Sequencing reads (Accession number CP002621.1) mapping to predicted open reading frames (ORFs) were quantified using HTSeq
Counts for ribosomal and transfer RNA sequences were filtered out of the data set and differential expression analyses were performed in R (version 2.15.1) using the Bioconductor package, edgeR
Significantly differentially expressed genes were determined using a P-value and false discovery rate (FDR) cut-off of 0.05.
We annotated differentially expressed genes using a combination of KEGG annotations, as well as manual annotation using operon and other functional data from the literature and E. faecalis OG1RF database available on BioCyc
Assembly: RNA sequencing reads were mapped to the E. faecalis OG1RF reference genome (NCBI accession: NC_017316.1) using BWA (v0.5.9) with default parameters
Supplementary files format and content: tab-delimited text file includes raw counts, log2-fold change, and p-value and FDR for each strain/condition, as well as gene name and annotation if applicable.

source_name: bacterial cell

growth_protocol: Strains WT, ∆srtA, ∆htrA, ∆srtA∆htrA, croR::tn∆srtA∆htrA,  ∆srtA∆htrA∆ebpABC cells were grown in TSB supplemented with 0.25% glucose and incubated static at 37°C until mid-exponential growth phase (OD600 0.5).

tag: mode of growth

value: bacterial cell


title: croR::tn∆srtA∆htrA, exponential, repl 2

description:
croR::tn∆srtA∆htrA 2 = 12535tndHdA_2a
croRtnsrtAhtrA vs srtAhtrA comparison.xlsx

value: planktonic bacteria


title: p47_ms_tigit


title: croR::tn∆srtA∆htrA, exponential, repl 1

description:
croR::tn∆srtA∆htrA 1 = 12535tndHdA_1a
croRtnsrtAhtrA vs srtAhtrA comparison.xlsx


title: in vivo, replicate 5, targeted DNA-Seq

description: in vivo


title: in vivo, replicate 4, targeted DNA-Seq

description: in vivo


title: WT BrdU 25C 30' sonication add S.pombe spike in rep1 [Alb835_WT_BrdU_S30]

description: add S.pombe spike in


title: ∆srtA∆htrA, exponential, repl 3   - repeat

description:
sequenced again for comparison with croR::tn∆srtA∆htrA strain, ∆srtA∆htrA 3 = dAdH_3
croRtnsrtAhtrA vs srtAhtrA comparison.xlsx


title: in vivo, replicate 3, targeted DNA-Seq

description: in vivo


title: WT input 25C 30' MNase add S.pombe spike in rep5 [Alb1036_WT_input_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: p41_ms_tigit


title: p42_ms_tigit


title: p40_ms_tigit


title: ∆srtA∆htrA, exponential, repl 2   - repeat

description:
sequenced again for comparison with croR::tn∆srtA∆htrA strain, ∆srtA∆htrA 2 = dAdH_2
croRtnsrtAhtrA vs srtAhtrA comparison.xlsx

value: Exponential phase


title: d0, replicate 3.2, targeted DNA-Seq

description: in vitro

value: day 0


title: WT input 25C 30' MNase add S.pombe spike in rep4 [Alb1012_WT_input_S30]

description: add S.pombe spike in

value: WT

value: input


title: WT input 25C 30' MNase add S.pombe spike in rep3 [Alb968_WT_input_S30]

description: add S.pombe spike in


title: ∆srtA∆htrA, exponential, repl 1  - repeat

description:
sequenced again for comparison with croR::tn∆srtA∆htrA strain, ∆srtA∆htrA 1 = dAdH_1
croRtnsrtAhtrA vs srtAhtrA comparison.xlsx


title: ∆srtA∆htrA, exponential, repl 3

description:
∆srtA∆htrA 3 = REB182
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx


title: in vivo, replicate 2, targeted DNA-Seq

description: in vivo

value: breast

value: female


title: WT BrdU 25C 30' sonication add S.pombe spike in rep2 [Alb897_WT_BrdU_S30]

description: add S.pombe spike in


title: WT Input 25C 30' MNase add S.pombe spike in rep2 [Alb886_WT_Input_S30]

description: add S.pombe spike in


title: p20_ms_tigit

value: Peripheral blood


title: d0, replicate 2, targeted DNA-Seq

description: in vitro


title: p16_ms_tigit

value: TIGIT+ memory B (TIM-1- TIGIT+) cells


title: ∆srtA∆htrA, exponential, repl 1

description:
∆srtA∆htrA 1 = REB174
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx

value: {delta}srtA{delta}htrA


title: ∆srtA∆htrA, exponential, repl 2

description:
∆srtA∆htrA 2 = REB178
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx


title: p38_ms_tigit


title: pre-treated, d20, PTX, targeted DNA-Seq

description: in vitro

value: day 20


title: p37_ms_tigit


title: ∆htrA, exponential, repl 3

description:
∆htrA 3 = REB180
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx

value: {delta}hrtA


title: ∆htrA, exponential, repl 2

description:
∆htrA 2= REB176
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx


title: WT BrdU 25C 30' MNase add S.pombe spike in rep3 [Alb978_WT_BrdU_S30]

description: add S.pombe spike in

value: BrdU


title: WT BrdU 25C 30' MNase add S.pombe spike in rep5 [Alb1044_WT_BrdU_S30]

description: add S.pombe spike in


title: WT BrdU 25C 30' MNase add S.pombe spike in rep4 [Alb1024_WT_BrdU_S30]

description: add S.pombe spike in


title: d0, replicate 1.2, targeted DNA-Seq

description: in vitro

value: Breast epithelial cell


title: p17_ms_tigit


title: p36_ms_tigit


title: pre-treated, d10, PTX, targeted DNA-Seq

description: in vitro

value: paclitaxel

value: day 10


title: ∆htrA, exponential, repl 1

description:
∆htrA 1 = REB172
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx

value: planktonic bacteria

value: bacterial cell


title: p35_hc_tigit


title: WT BrdU 25C 30' MNase add S.pombe spike in rep2 [Alb898_WT_BrdU_S30]

description: add S.pombe spike in

value: 25C 30' MNase


title: in vivo, replicate 1, targeted DNA-Seq

description: in vivo


title: pre-treated, d3, PTX, targeted DNA-Seq

description: in vitro

value: day 3


title: WT Input 25C 30' MNase add S.pombe spike in rep1 [Alb824_WT_Input_S30]

description: add S.pombe spike in

value: WT

value: Input


title: ∆srtA, exponential, repl 2

description:
∆srtA 2 = REB177
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx

value: {delta}srtA

value: Exponential phase


title: WT BrdU 25C 30' Mnase add S.pombe spike in rep1 [Alb836_WT_BrdU_S30]

description: add S.pombe spike in


title: ∆srtA, exponential, repl 1

description:
∆srtA 1 = REB173
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx


title: p33_hc_tigit

value: Peripheral blood


title: pre-treated, d0, replicate 2, targeted DNA-Seq

description: in vitro

value: breast

value: female

value: day 0


title: Donor-E_CD8-T-cells_RFP-overexpression_unstim

city: Woluwe Waint Lambert

first: Pierre

last: van der Bruggen

address: Avenue Hippocrate 75

country: Belgium

institute: de Duve institute

description:
Donor-E = TERF = LB6019
TERF_RFP_unstim

data_processing:
Quality control
Files were trimmed with trimmomatic
aligned to GRCh38 human genome with HISAT2
Read counts were determined with featuresCount
Normalization of read counts and analysis of differentially expressed genes were performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: DSEq2_IRF4_KO_normalized.csv
Supplementary files format and content: DSEq2_IRF4_OE_normalized.csv

molecule: polyA RNA

source_name: Blood

growth_protocol: CD8 T-cells were lentivirally transduced or nucleofected with gRNA on the same day as they were activated with anti-CD3/CD28 beads and amplified in IMDM + human serum 10% + glutamax 1,5mM + Pénicilline 100U/ml + Streptomycin 100ug/ml + IL-2 50U/ml. Cells were reactivated or not with anti-CD3 (OKT3 clone) for 5h, stained, fixed and permeabilized, and stained again to sort IRF4 knock-out or IRF4 overexpressing cells, and their respective control counterparts

extract_protocol:
RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (ref AM1975 Thermo Fisher Scientific)
SMART-Seq (Nextera XT DNA Library Preparation Kit (96 samples)  FC-131-1096, Illumina). PolyA-RNA, unstranded library

treatment_protocol: 5h coated anti-CD3 (1ug/ml)

tag: individual

value: Donor-E

value: Blood

value: Primary CD8 T cells

tag: genetic modification

value: RFP overexpression

tag: stimulation

value: unstimulated


title: p32_hc_tigit

tag: tissue

value: TIGIT+ memory B (TIM-1- TIGIT+) cells


title: pre-treated, d17, PTX, targeted DNA-Seq

description: in vitro

tag: cell line

value: Breast epithelial cell

tag: Sex

value: paclitaxel

value: day 17


title: pre-treated, d0, replicate 1, targeted DNA-Seq

description: in vitro

tag: treatment

tag: time


title: Donor-E_CD8-T-cells_RFP-overexpression_OKT3

description:
Donor-E = TERF = LB6019
TERF_RFP_OKT3

tag: cell type


title: WT, exponential, repl 2

description:
WT 2 = REB175
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx

value: planktonic bacteria

value: bacterial cell

value: WT


title: p30_hc_tigit


title: d15, PTX, replicate 3.4, targeted DNA-Seq

description: in vitro

value: day 15


title: p31_hc_tigit

value: Peripheral blood


title: WT, exponential, repl 1

description:
WT 1 = REB171
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx

value: Exponential phase


title: p34_hc_tigit


title: p22_ms_tigit


title: Donor-E_CD8-T-cells_IRF4-overexpression_OKT3

description:
Donor-E = TERF = LB6019
TERF_IRF4_OKT3

value: IRF4 overexpression


title: Donor-E_CD8-T-cells_IRF4-overexpression_unstim

description:
Donor-E = TERF = LB6019
TERF_IRF4_unstim


title: Donor-B_CD8-T-cells_RFP-overexpression_unstim

description:
Donor-B = SUYD = LB9481
SUYD_RFP_unstim

value: Donor-B


title: ∆srtA, exponential, repl 3

description:
∆srtA 3 = REB181
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx

value: {delta}srtA


title: d15, PTX, replicate 3.3, targeted DNA-Seq

description: in vitro

value: breast

value: female


title: p21_ms_tigit


title: WT, Daptomycin, repl 3

description:
WT-DAP1-E2
WT DAP vs untreated.xlsx

value: Daptomycin


title: d15, PTX, replicate 3.2, targeted DNA-Seq

description: in vitro


title: Donor-B_CD8-T-cells_RFP-overexpression_OKT3

description:
Donor-B = SUYD = LB9481
SUYD_RFP_OKT3

value: Blood

value: Primary CD8 T cells

value: RFP overexpression


title: WT, Daptomycin, repl 2

description:
WT-DAP1-E1
WT DAP vs untreated.xlsx


title: p29_hc_tigit

value: TIGIT+ memory B (TIM-1- TIGIT+) cells


title: WT, exponential, repl 3

description:
WT 3 = REB179
WT_dhtrA_dsrtA_dsrtAdhtrA comparisons.xlsx


title: d15, PTX, replicate 3.5, targeted DNA-Seq

description: in vitro

value: Breast epithelial cell

value: paclitaxel


title: d15, PTX, replicate 3.1, targeted DNA-Seq

description: in vitro


title: p18_ms_tigit


title: d15, replicate 3.3, targeted DNA-Seq

description: in vitro


title: Donor-B_CD8-T-cells_IRF4-overexpression_unstim

description:
Donor-B = SUYD = LB9481
SUYD_IRF4_unstim

value: unstimulated


title: WT, Daptomycin, repl 1

description:
WT-DAP1-D
WT DAP vs untreated.xlsx

value: planktonic bacteria

value: bacterial cell

value: WT


title: Donor-B_CD8-T-cells_IRF4-overexpression_OKT3

description:
Donor-B = SUYD = LB9481
SUYD_IRF4_OKT3


title: d15, replicate 3.2, targeted DNA-Seq

description: in vitro

value: day 15


title: Donor-A_CD8-T-cells_RFP-overexpression_unstim

description:
Donor-A = PULU = LB3149
PULU_RFP_unstim

value: Donor-A


title: p15_ms_tigit

value: Peripheral blood


title: WT, untreated, repl 3

description:
d12-noDAP-C2
WT DAP vs untreated.xlsx

value: Exponential phase

value: untreated


title: WT, untreated, repl 1

description:
d12-noDAP-A
WT DAP vs untreated.xlsx


title: WT, untreated, repl 2

description:
d12-noDAP-C1
WT DAP vs untreated.xlsx


title: d0, replicate 3, targeted DNA-Seq

description: in vitro

value: breast

value: female

value: day 0


title: Donor-A_CD8-T-cells_RFP-overexpression_OKT3

description:
Donor-A = PULU = LB3149
PULU_RFP_OKT3

value: Blood

value: Primary CD8 T cells


title: p23_hc_tigit

value: TIGIT+ memory B (TIM-1- TIGIT+) cells


title: rad26elf1_uv2hr_A5

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Background values dipyrimidine sequences were generated in WIG file using custom perl script
Assembly: SacCer3
Supplementary files format and content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences and including background value of 0.0 at nucleotides associated with dipyrimidines with no mapped sequencing reads. A sequencing read count was assigned to each nucleotide in the lesion-containing dipyrimidine sequence. For no UV (untreated samples), just a txt file with dinucleotide counts are provided

source_name: Yeast cells

growth_protocol: Yeast cultures containing the indicated mutants were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 5 μg of DNA was used for each sequencing library preparation.
CPD-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.
OTHER (CPD-seq)

treatment_protocol: Yeast cells were harvested and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. Following UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) to allow for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at 2 hours after UV irradiation (2hr). Cells were spun down and stored at -80˚C until genomic DNA isolation.

value: Yeast cells

value: rad26-delta elf1-delta

value: UV irradiated 125 J/m2

tag: repair time

value: 2 hr


title: p14_ms_tigit

tag: patient


title: d15, PTX, replicate 2.3, targeted DNA-Seq

description: in vitro

value: Breast epithelial cell

value: paclitaxel


title: p24_hc_tigit


title: rad26elf1_nouv_A6


title: d15, PTX, replicate 2.2, targeted DNA-Seq

description: in vitro

value: day 15


title: Donor-C_CD8-T-cells_RFP-overexpression_unstim

description:
Donor-C = LAMD = LB5660
LAMD_RFP_unstim

value: Donor-C

value: RFP overexpression

value: unstimulated


title: p1_ms_tigit

value: Peripheral blood


title: p9_ms_tigit


title: d15, PTX, replicate 2.1, targeted DNA-Seq

description: in vitro

value: breast


title: d15, replicate 3.1, targeted DNA-Seq

description: in vitro

value: female


title: shGATA2AS12_day14_2

city: Bethesda

first: Ann

last: Dean

state: MD

address: 50 South Drive, Bldg 50

department: NIDDK

institute: NIH

data_processing:
For HUDEP2 RNA-seq, raw sequence reads were trimmed with cutadapt v3.4 to remove any adapters with trimming parameters "-a AGATCGGAAGAGCACACGT -q 20 --minimum-length=25". Trimmed reads were quantified with kallisto v0.46.2 with pre-built index of human Ensembl v96 transcriptomes provided by pachterlab github website. Differential expression was tested using R v4.1.0 with DESeq2 v1.32.0.  MA plot was produced with ggplot2. GO analysis was performed with clusterProfiler v4.0.5.
For CD34 RNA-seq, raw sequence reads were trimmed with cutadapt v4.4 to remove any adapters with parameters "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim 20 --minimum-length=25". Trimmed reads were aligned to human genome Gencode v43 using hisat2 (v2.2.1), and quatifified with featureCounts (v.2.0.3). Differential expression was performed using R v4.3.1 with DESeq2 v1.40.2.
For ChIP-seq and ChIRP-seq, raw sequence reads were trimmed with cutadapt v3.4 with trimming parameters "-a CTGTCTCTTATACACATCT -q 20 --minimum-length=25". Trimmed reads were aligned with Bowtie2 v2.4.4 to pre-built human NCBI GRCh38 index provided by Bowtie website with parameter “--very-sensitive". Multimapping reads and duplicate reads were removed with sambamba v0.6.8 and picard v2.26.10. BigWig files were created with deepTools v3.5.1 using bamCoverage tool with the additional arguments “--binSize 10 --normalizeUsing CPM --extendReads 300”. Peaks were called for each replicate individually using macs v2.2.7.1. Conserved peaks were obtained from intersections between replicates by using BEDTools v2.30.0. Differential binding sites were obtained by DiffBind v3.2.7.
For ATAC-seq, Paired-end raw sequence reads were trimmed with cutadapt v3.4 with trimming parameters "-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -q 20 --minimum-length=25". Trimmed reads were aligned with Bowtie2 v2.4.4 to pre-built human NCBI GRCh38 index provided by Bowtie website with parameter “--sensitive". Multimapping reads and duplicate reads were removed with sambamba v0.6.8 and picard v2.26.10. BigWig files were created with deepTools v3.5.1 using bamCoverage tool with the additional arguments “--binSize 10 --normalizeUsing CPM”. Peaks were called for each replicate individually using macs v2.2.7.1 with parameters “--nomodel --shift 100 --extsize 200”. Conserved peaks were obtained from intersections between replicates by using BEDTools v2.30.0. Differential binding sites were obtained by DiffBind v3.2.7.
Assembly: hg38
Supplementary files format and content: Text file contains raw featureCount, Csv files contain differential expressed genes from RNAseq results. Bed files contain differential binding sites.

growth_protocol: HUDEP2 cells were cultured as described(Vinjamur, D.S. and Bauer, D.E., 2018, Methods Mol Biol). Cells were cultured in serum-free expansion medium (SFEMII, STEMCELL Technologies, 09655) supplemented with  50 ng/mL human stem cell factor (R&D Systems, 255-SC), 3 units/mL erythropoietin (AMGEN), 10−6 M dexamethasone (Sigma-Aldrich, D2915)  and 1ug/ml doxycycline (Clontech, 631311). Cells were induced in EDM2 medium for 4 days, EDM3 medium for 3 days and EDM medium for 2 days.  Primary CD34+ umbilical cord cells were obtained from Lonza (cat. 2C-101) and were cultured as described (The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).)

extract_protocol:
RNA was extracted by PureLink RNA mini kit (Invitrogen, 12183020), and DNA was removed by DNase digestion (Invitrogen, 12185-010).
For RNA sequencing, libraries were constructed from 500ng total RNA by using the Truseq Stranded mRNA sample preparation kit (Illumina 20020493). ChIPmentatation were performed as described previously (Krivega and Dean, 2018a; Schmidl et al., 2015). ATAC-seq was performed according to Corces, M.R. et al, 2017, Nature Methods.

treatment_protocol: To knockout GATA2AS in Hudep2 cells, pSpCas9-2A-GFP plasmid (Addgene #4813) containing guide RNAs targeting transcription start site of the GATA2AS gene was electroporated into Hudep2 cells with Lonza Nucleofector Kit V (VCA-1003). Single cell clones were isolated and genotyped. The indel fragment was amplified and sequenced by Sanger sequencing. To knockdown GATA2AS in CD34+ cells, shRNAs were transduced at day 5.

tag: cell line/strain

value: knockdown GATA2AS12

tag: age

value: day 14


title: Donor-C_CD8-T-cells_RFP-overexpression_OKT3

description:
Donor-C = LAMD = LB5660
LAMD_RFP_OKT3

value: Blood

value: Primary CD8 T cells


title: rad26elf1_uv0hr_A4

value: Yeast cells

value: 0 hr


title: d15, replicate 2.3, targeted DNA-Seq

description: in vitro


title: p33_hc_breg_dp_rep

value: double positive memory B (TIM-1+TIGIT+) cells


title: Donor-A_CD8-T-cells_IRF4-overexpression_unstim

description:
Donor-A = PULU = LB3149
PULU_IRF4_unstim

value: Donor-A

value: IRF4 overexpression


title: shGATA2AS12_day14_1


title: d15, replicate 2.2, targeted DNA-Seq

description: in vitro

value: Breast epithelial cell


title: p30_hc_breg_dp_rep


title: Donor-A_CD8-T-cells_IRF4-overexpression_OKT3

description:
Donor-A = PULU = LB3149
PULU_IRF4_OKT3


title: Donor-C_CD8-T-cells_IRF4-overexpression_unstim

description:
Donor-C = LAMD = LB5660
LAMD_IRF4_unstim


title: Donor-C_CD8-T-cells_IRF4-overexpression_OKT3

description:
Donor-C = LAMD = LB5660
LAMD_IRF4_OKT3


title: shGATA2AS11_day14_2

value: knockdown GATA2AS11


title: p59_ms_breg_dp


title: shGATA2AS11_day14_1


title: p55_ms_breg_dp


title: d15, replicate 2.1, targeted DNA-Seq

description: in vitro

value: day 15


title: d0, replicate 2.2, targeted DNA-Seq

description: in vitro

value: day 0


title: Donor-D_CD8-T-cells_RFP-overexpression_unstim

description:
Donor-D = FORD = LB9847
FORD_RFP_unstim

value: Donor-D

value: RFP overexpression

value: unstimulated


title: Donor-D_CD8-T-cells_RFP-overexpression_OKT3

description:
Donor-D = FORD = LB9847
FORD_RFP_OKT3


title: p53_ms_breg_dp

value: Peripheral blood


title: Donor-D_CD8-T-cells_IRF4-overexpression_unstim

description:
Donor-D = FORD = LB9847
FORD_IRF4_unstim


title: p51_ms_breg_dp


title: Donor-D_CD8-T-cells_IRF4-overexpression_OKT3

description:
Donor-D = FORD = LB9847
FORD_IRF4_OKT3


title: shControl_day14_2

value: knockdown control


title: shControl_day14_1

value: day 14


title: d17, PTX, replicate 1, targeted DNA-Seq

description: in vitro

value: breast

value: female

value: paclitaxel

value: day 17


title: p47_ms_breg_dp

value: double positive memory B (TIM-1+TIGIT+) cells


title: Donor-D_CD8-T-cells_IRF4-gRNA_unstim

description:
Donor-D = FORD = LB9847
14-A12-IRF4-20

value: Blood

value: Primary CD8 T cells


title: shGATA2AS12_day10_1

value: knockdown GATA2AS12

value: day 10


title: Donor-B_CD8-T-cells_IRF4-gRNA_unstim

description:
Donor-B = SUYD = LB9481
14-A11-IRF4-19

value: Donor-B


title: p46_ms_breg_dp


title: shGATA2AS11_day10_1

value: knockdown GATA2AS11


title: shGATA2AS12_day10_2


title: d13, PTX, replicate 1, targeted DNA-Seq

description: in vitro

value: Breast epithelial cell

value: day 13


title: Donor-C_CD8-T-cells_IRF4-gRNA_unstim

description:
Donor-C = LAMD = LB5660
14-A9-IRF4-17

value: Donor-C

value: unstimulated


title: shControl_day10_2

value: knockdown control


title: d3, PTX, replicate 1, targeted DNA-Seq

description: in vitro

value: day 3


title: shGATA2AS11_day10_2


title: d0, replicate 1, targeted DNA-Seq

description: in vitro

value: breast

value: day 0


title: Donor-E_CD8-T-cells_IRF4-gRNA_unstim

description:
Donor-E = TERF = LB6019
14-A10-IRF4-18

value: Donor-E


title: p16_ms_breg_dp

value: Peripheral blood


title: d9, PTX, replicate 1, targeted DNA-Seq

description: in vitro

value: female

value: paclitaxel

value: day 9


title: Donor-A_CD8-T-cells_IRF4-gRNA_unstim

description:
Donor-A = PULU = LB3149
14-A8-IRF4-16

value: Donor-A

value: Blood

value: Primary CD8 T cells


title: d0, replicate 2.1, targeted DNA-Seq

description: in vitro


title: d24, PTX, replicate 1, targeted DNA-Seq

description: in vitro

value: day 24


title: p44_ms_breg_dp

value: double positive memory B (TIM-1+TIGIT+) cells


title: p20_ms_breg_dp


title: shControl_day10_1

value: day 10


title: sox9-tfn_exp3

city: Saint Louis

first: Charles

middle: K

last: Kaufman

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

data_processing:
Assess read quality with FastQC
Align to hg38 using STAR
Quantify transcriptome using RSEM
Normalize reads with DESeq2
Assembly: hg38
Supplementary files format and content: counts per million file, differential expression file

source_name: Melanoma

growth_protocol: A375 cells were grown and split according to standard protocols until treatment.

extract_protocol:
Scraped cells into an Eppendorf tube, counted cells, and allocated 1 million cells for RNA-seq preparation.
Extracted total RNA using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transfected cells treated with 1:3 ratio of SOX9-HA DNA:PEI transfection reagent in Opti-MEM for 48 hours (unless otherwise noted), then collected

value: Melanoma

tag: strain

value: Transfected with 5µg SOX9-HA

tag: length of treatment

value: 48 hours


title: p37_ms_breg_dp


title: Donor-D_CD8-T-cells_IRF4-gRNA_OKT3

description:
Donor-D = FORD = LB9847
14-A7-IRF4-15

value: Donor-D


title: sox9-tfn_exp2


title: Donor-B_CD8-T-cells_IRF4-gRNA_OKT3

description:
Donor-B = SUYD = LB9481
14-A6-IRF4-14

value: Donor-B


title: p38_ms_breg_dp


title: p17_ms_breg_dp


title: sox9-tfn_atac


title: Donor-E_CD8-T-cells_IRF4-gRNA_OKT3

description:
Donor-E = TERF = LB6019
14-A5-IRF4-13


title: pei-only-tfn_exp1

value: Non-transfected


title: shGATA2AS11_day6_2

value: knockdown GATA2AS11

value: day 6


title: p35_hc_breg_dp

value: Peripheral blood


title: shGATA2AS11_day6_1


title: p34_hc_breg_dp


title: Donor-C_CD8-T-cells_IRF4-gRNA_OKT3

description:
Donor-C = LAMD = LB5660
14-A4-IRF4-12

value: Donor-C

value: IRF4 knock-out


title: Donor-A_CD8-T-cells_IRF4-gRNA_OKT3

description:
Donor-A = PULU = LB3149
14-A3-IRF4-11

value: Donor-A


title: no-tfn_exp3


title: no-tfn_exp2


title: p36_ms_breg_dp


title: shControl_day6_1

value: knockdown control


title: p32_hc_breg_dp


title: no-tfn_exp1


title: shControl_day6_2


title: kogata2as_ATACseq_r2

data_processing:
For RNA-seq, Raw sequence reads were trimmed with cutadapt v3.4 to remove any adapters with trimming parameters "-a AGATCGGAAGAGCACACGT -q 20 --minimum-length=25". Trimmed reads were quantified with kallisto v0.46.2 with pre-built index of human Ensembl v96 transcriptomes provided by pachterlab github website. Differential expression was tested using R v4.1.0 with DESeq2 v1.32.0.  MA plot was produced with ggplot2. GO analysis was performed with clusterProfiler v4.0.5.
For ChIP-seq and ChIRP-seq, raw sequence reads were trimmed with cutadapt v3.4 with trimming parameters "-a CTGTCTCTTATACACATCT -q 20 --minimum-length=25". Trimmed reads were aligned with Bowtie2 v2.4.4 to pre-built human NCBI GRCh38 index provided by Bowtie website with parameter “--very-sensitive". Multimapping reads and duplicate reads were removed with sambamba v0.6.8 and picard v2.26.10. BigWig files were created with deepTools v3.5.1 using bamCoverage tool with the additional arguments “--binSize 10 --normalizeUsing CPM --extendReads 300”. Peaks were called for each replicate individually using macs v2.2.7.1. Conserved peaks were obtained from intersections between replicates by using BEDTools v2.30.0. Differential binding sites were obtained by DiffBind v3.2.7.
For ATAC-seq, Paired-end raw sequence reads were trimmed with cutadapt v3.4 with trimming parameters "-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -q 20 --minimum-length=25". Trimmed reads were aligned with Bowtie2 v2.4.4 to pre-built human NCBI GRCh38 index provided by Bowtie website with parameter “--sensitive". Multimapping reads and duplicate reads were removed with sambamba v0.6.8 and picard v2.26.10. BigWig files were created with deepTools v3.5.1 using bamCoverage tool with the additional arguments “--binSize 10 --normalizeUsing CPM”. Peaks were called for each replicate individually using macs v2.2.7.1 with parameters “--nomodel --shift 100 --extsize 200”. Conserved peaks were obtained from intersections between replicates by using BEDTools v2.30.0. Differential binding sites were obtained by DiffBind v3.2.7.
Assembly: hg38
Supplementary files format and content: Csv files contain differential expressed genes from RNAseq results. Bed files contain differential binding sites.

growth_protocol: HUDEP2 cells were cultured as described(Vinjamur, D.S. and Bauer, D.E., 2018, Methods Mol Biol). Cells were cultured in serum-free expansion medium (SFEMII, STEMCELL Technologies, 09655) supplemented with  50 ng/mL human stem cell factor (R&D Systems, 255-SC), 3 units/mL erythropoietin (AMGEN), 10−6 M dexamethasone (Sigma-Aldrich, D2915)  and 1ug/ml doxycycline (Clontech, 631311). Cells were induced in EDM2 medium for 4 days, EDM3 medium for 3 days and EDM medium for 2 days.

treatment_protocol: To knockout GATA2AS in Hudep2 cells, pSpCas9-2A-GFP plasmid (Addgene #4813) containing guide RNAs targeting transcription start site of the GATA2AS gene was electroporated into Hudep2 cells with Lonza Nucleofector Kit V (VCA-1003). Single cell clones were isolated and genotyped. The indel fragment was amplified and sequenced by Sanger sequencing.

tag: chip antibody

tag: genotype

value: knockout GATA2AS


title: Donor-B_CD8-T-cells_ctrl-gRNA_unstim

description:
Donor-B = SUYD = LB9481
14-A1-IRF4-9

tag: individual

value: Blood

value: Primary CD8 T cells

value: control

value: unstimulated


title: Donor-D_CD8-T-cells_ctrl-gRNA_unstim

description:
Donor-D = FORD = LB9847
14-A2-IRF4-10

tag: genetic modification


title: shGATA2AS12_day6_2

value: knockdown GATA2AS12


title: p31_hc_breg_dp

value: double positive memory B (TIM-1+TIGIT+) cells


title: shGATA2AS12_day6_1


title: Donor-E_CD8-T-cells_ctrl-gRNA_unstim

description:
Donor-E = TERF = LB6019
13-B4-IRF4-8

value: Donor-E

tag: stimulation


title: no-tfn_atac

value: Melanoma

value: 48 hours


title: kogata2as_ATACseq_r1


title: p29_hc_breg_dp

tag: tissue


title: 24h_10ug-dna-tfn_exp2

value: Transfected with 10µg SOX9-HA

value: 24 hours


title: Donor-C_CD8-T-cells_ctrl-gRNA_unstim

description:
Donor-C = LAMD = LB5660
13-B3-IRF4-7


title: p22_ms_breg_dp

value: Peripheral blood


title: koctrl_ATACseq_r1

value: knockout control


title: 10ug-dna-tfn_exp1


title: Donor-A_CD8-T-cells_ctrl-gRNA_unstim

description:
Donor-A = PULU = LB3149
13-B2-IRF4-6


title: 5ug-dna-tfn_exp1

value: Transfected with 5µg SOX9-HA


title: Donor-D_CD8-T-cells_ctrl-gRNA_OKT3

description:
Donor-D = FORD = LB9847
13-B1-IRF4-5

value: Donor-D


title: p21_ms_breg_dp


title: p15_ms_breg_dp


title: kogata2as_H3K27ac_ChIPseq_r2

value: H3K27ac (Abcam, ab4729)


title: 2.5ug-dna-tfn_exp1

value: Transfected with 2.5µg SOX9-HA


title: Donor-B_CD8-T-cells_ctrl-gRNA_OKT3

description:
Donor-B = SUYD = LB9481
13-A12-IRF4-4

value: Donor-B

value: Blood


title: kogata2as_H3K27ac_ChIPseq_r1

value: knockout GATA2AS


title: Donor-E_CD8-T-cells_ctrl-gRNA_OKT3

description:
Donor-E = TERF = LB6019
13-A11-IRF4-3

value: Primary CD8 T cells

value: control


title: p18_ms_breg_dp

value: double positive memory B (TIM-1+TIGIT+) cells


title: Donor-C_CD8-T-cells_ctrl-gRNA_OKT3

description:
Donor-C = LAMD = LB5660
13-A10-IRF4-2

value: Donor-C


title: A375_HA_SOX9_HA_R3

data_processing:
For rounds 2 and 3 (R2 and R3 of transfection), the 2 "read 1" fastq files (one from each lane) were concatenated and the 2 "read 2" fastq files were concatenated
Demultiplex and trim reads with Cutadapt
Align reads to hg38 using bowtie2
Reads sorted with samtools
Duplicate reads removed with Picard
Call peaks and normalize to IgG using MACS2
Index BAM files with samtools
Generate bigwigs with deepTools bamCoverage
Assembly: hg38
Supplementary files format and content: bigwig and narrowpeak

extract_protocol:
50,000 cells were collected from each condition and processed using the Epicypher CUTANA ChIC/CUT&RUN kit (cat #14-1048)
Library was prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (cat #E7645S) with NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 (cat #E7600S)
CUT&RUN
For rounds 2 and 3 (R2 and R3), samples were all pooled together and then run on 2 lanes, resulting in 4 files for each sample -- 2 "read 1" files and 2 "read 2" files

value: Melanoma

tag: antibody

value: HA

tag: date of sequencing

tag: round of transfection


title: koctrl_H3K27ac_ChIPseq_r1


title: koctrl_H3K27ac_ChIPseq_r2


title: A375_SOX10_SOX9_HA_R3

tag: treatment


title: kogata2as_KLF1_ChIPseq_r2

value: KLF1 (Abcam, ab2483)


title: p24_hc_breg_dp

tag: cell type


title: Donor-A_CD8-T-cells_ctrl-gRNA_OKT3

description:
Donor-A = PULU = LB3149
13-A9-IRF4-1

value: Donor-A


title: koctrl_ATACseq_r2


title: p14_ms_breg_dp

value: Peripheral blood


title: A375_SOX9_SOX9_HA_R3


title: A375_IgG_SOX9_HA_R3

value: IgG


title: kogata2as_KLF1_ChIPseq_r1


title: p9_ms_breg_dp


title: shVDR, 10h, rep3

city: Jinan City

first: Yan

last: Xu

address: No. 44 Wenhua West Road

country: China

institute: Shandong University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)   by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4) .
Bowtie2 (v2.2.5)   was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Text Document  include Raw read counts for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ  platform.

tag: cell line

value: VDR knockdown


title: A375_H3K4me3_SOX9_HA_R3


title: shVDR, 10h, rep2


title: kogata2as_KLF1_ChIPseq_Input


title: shVDR, 10h, rep1


title: BE2, 1day 2uM ATRA, SMAD4 ChIP, input

city: Cordova

first: YINWEN

last: ZHANG

state: TN

address: 2189 Purple Leaf Ln

institute: stjude research hospital

data_processing:
bcl2fastq v2.20.0.422 was applied for converting per-cycle BCL basecall files to per-read fastq files
trimgalore v0.4.4 was applied to remove low quality reads and adaptor with default setting
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA mem v0.7.17 with default setting
To generate genome-wide coverage profiles, the bedtools v2.17.0 “genomecov” command was applied , and the output was converted to bigwig files using bedGraphToBigWig
MACS2 v2.1.1 was utilized to identify ChIP-seq signal enriched regions (narrow peaks) with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: BigWig, narrowPeak(except for input sample)

growth_protocol: All cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cross-linking: After desired treatment, cells were incubated with 1% formaldehyde to crosslink the proteins and DNA. Glycine was added to a final concentration of 225 mM to quench the reaction. 20 million cells were used for each sample. Chromatin shearing: The cells were lysed with Covaris Lysis buffer (0.25% Triton X-100, 1 mM EDTA pH 8.0, 140 mM NaCl, 50 mM HEPES pH 7.9, 10% glycerol, 0.5% NP-40). The chromatins were collected by centrifuge and the pellets were washed 2 time with Covaris Wash Buffer (1 mM EDTA pH 8.0, 10 mM Tris HCl pH 8.0, 200 mM NaCl, 0.5 mM EGTA pH 8.0) and 2 times with Covaris Shearing Buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris HCl pH 8.0). Then the chromatins were sheared to 200 – 700 bp in Covaris Shearing Buffer with the ultrasonicator Covaris LE220 (Covaris, Woburn, MA).  Immunoprecipitation: Protein A/G-coated magnetic beads (protein A-coated beads (Diagenode, # C03010020-150) for rabbit antibody; protein G-coated beads (Diagenode, # C03010021-150) for mouse antibody) were washed with 0.5% BSA in PBS (g/ml) and added to the sheared chromatin to preclean the samples by rotation at 4°C for 1 hour. 100 µl of the beads were used for each sample. The magnetic beads were isolated with a magnetic separation rack and the supernatant was collected for immunoprecipitation. Primary antibodies were added to the samples, then the samples were incubated at 4°C overnight with rotation. The antibodies used in this study are HA (Cell Signaling, # 3724; use 40 µl of antibody for each sample in 2 ml of buffer (1:50 dilution)), SMAD4 (R&D Systems, # AF2097; use 20 µg per 20 million cells), and RARA (R&D Systems, # PP-H1920-00; use 20 µg per 20 million cells). On the second day, 100 µl of freshly washed protein A/G-coated magnetic beads were added to each sample. Then the samples were incubated at 4°C for 5 h with rotation. Elution and reverse cross-links: The beads were collected and washed for 1 time with cold Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl), 2 times with cold High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 500 mM NaCl), 1 time with cold LiCl Wash Buffer (1 mM EDTA, 10 mM Tris pH 8.0, 250 mM LiCl, 1% NP-40, 1% DOC), and 2 times with cold TE Buffer pH 8.0 (1 mM EDTA, 10 mM Tris pH 8.0). Then the DNA were eluted from the beads with 100 µl of freshly made Elution buffer (0.1 M NaHCO3 and 1% SDS). 4 µl of 5M NaCl and 2 µl of RNaseA (10 mg/mL) (ThermoFisher, # EN0531) were added to each sample and the samples were then incubated at 65°C with shaking overnight. DNA purification: Proteins in the samples were removed by adding 5 µg of proteinase K (ThermoFisher, # AM2548) and shaking at 60°C for 2 hours. Afterward, the DNA was purified with Qiagen MinElute PCR Purification Kit (Qiagen, # 28004).
ChIP-seq DNA libraries were prepared using the KAPA HyperPrep Kit (Roche, # KK8504) and sequenced on the Illumina NextSeq 500 system. At least 50 million reads were collected for each sample.

value: Neuroblastoma

value: 1 day 2uM ATRA


title: BE2, 1day 2uM ATRA, Replicate1, SMAD4 ChIP


title: koctrl_KLF1_ChIPseq_r1

value: knockout control


title: A375_SOX9_No_tfn_R3

value: No-tfn


title: A375_IgG_No_tfn_R3


title: BE2, DMSO, SMAD4 ChIP, input

value: DMSO control


title: koctrl_KLF1_ChIPseq_Input


title: shNC, 10h, rep3

value: shNC


title: BE2, 1day 2uM ATRA, Replicate2, SMAD4 ChIP


title: BE2, DMSO, Replicate2, SMAD4 ChIP


title: koctrl_KLF1_ChIPseq_r2


title: shNC, 10h, rep2


title: A375_H3K4me3_No_tfn_R3


title: kogata2as_LRF_ChIPseq_r2

value: LRF (Abcam, ab175918)

value: knockout GATA2AS


title: A375_HA_SOX9_HA_R2


title: kogata2as_LRF_ChIPseq_r1


title: Kang-Glut1sh-TGFb3

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th Ave NE

institute: The Hormel Institute

data_processing:
Illumina Real time Analysis and CASAVA software 1.8.2 were used for basecalling.
Raw reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control checks on raw sequence data for each sample were performed with FastQC.  Read mapping was performed via Bowtie (v2.2.4.0) using the Human genome (hg19) as reference
Raw reads for each gene generated from the HiSeq2500 sequencer were subjected to statistical analysis using the edgeR package and cuffdiff2 package based on two selection criteria (fold change ≥ 2 & FDR < 0.05, and fold change ≥ 1.5 & FDR < 0.01).  The overlap of these four criteria was used to identify genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cell expressing Glut1 shRNA + TGFbeta

growth_protocol: Cells obtained from ScienCell were cultured with DMEM supplemented with 10% FBS, streptomycin and penicillin.

extract_protocol:
RNA samples were isolated from the cells by using RNeasy Plus Mini kit (Qiagen, 74134) and gDNA Eliminator Columns were used to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing by using standard Illumina protocols

treatment_protocol: Cells were first subjected to serum-starvation for overnight and were incubated with TGFbeta1 (5 ng/ml) for 24 hours

value: Liver hepatic stellate cells

value: Glut1 shRNA

tag: tgfb1 treatment

tag: time


title: BE2, 1day 2uM ATRA, RARA ChIP, input


title: BE2 DMSO, Replicate1, SMAD4 ChIP


title: A375_SOX10_SOX9_HA_R2

value: Melanoma


title: kogata2as_LRF_H3K27ac_ChIPseq_Input

tag: cell line/strain


title: BE2, 1day 2uM ATRA, Replicate2, RARA ChIP


title: A375_SOX10_No_tfn_R3

tag: strain


title: A375_IgG_SOX9_HA_R2


title: Kang-Glut1sh-3

source_name: Cell expressing Glut1 shRNA


title: koctrl_LRF_H3K27ac_ChIPseq_Input


title: shNC, 10h, rep1


title: Kang-Glut1sh-2


title: BE2, DMSO, RARA ChIP, input


title: A375_H3K4me3_SOX9_HA_R2


title: koctrl_LRF_ChIPseq_r1


title: BE2, DMSO, Replicate2, RARA ChIP


title: Kang-Glut1sh-1


title: Kang-NT-TGFb3

source_name: Cell expressing control shRNA + TGFbeta

value: control shRNA


title: TGW, 3day 2uM ATRA, SMAD4 ChIP, input

source_name: TGW

value: TGW

value: 3 day 2uM ATRA


title: Kang-NT-TGFb2


title: A375_SOX10_No_tfn_R2


title: Kang-Glut1sh-TGFb2


title: BE2 DMSO, Replicate1, RARA ChIP


title: kogata2as_d9_RNAseq_r1

value: knockout GATA2AS on day 9


title: A375_SOX9_No_tfn_R2


title: koctrl_d9_RNAseq_r2

value: knockout control on day 9


title: kogata2as_d9_RNAseq_r2


title: Kang-Glut1sh-TGFb1


title: A375_IgG_No_tfn_R2

value: IgG


title: TGW, 3day 2uM ATRA, Replicate2, SMAD4 ChIP

value: Neuroblastoma


title: Kang-NT-TGFb1


title: A375_SOX9_SOX9_HA_R2


title: koctrl_LRF_ChIPseq_r2


title: BE2, 1day 2uM ATRA, Replicate1, RARA ChIP

value: 1 day 2uM ATRA


title: koctrl_d9_RNAseq_r1


title: Kang-NT3

source_name: Cell expressing control shRNA


title: SKMel5_Myc_SOX9_Myc_R1

value: Myc


title: kogata2as_d7_RNAseq_r2

value: knockout GATA2AS on day 7


title: TGW, 1day 2uM ATRA, SMAD4 ChIP, input


title: Kang-NT2


title: SKMel5_SOX10_SOX9_Myc_R1


title: kogata2as_d7_RNAseq_r1


title: TGW, 1day 2uM ATRA, Replicate2, SMAD4 ChIP


title: TGW, 1day 2uM ATRA, Replicate1, SMAD4 ChIP


title: koctrl_d7_RNAseq_r2

value: knockout control on day 7


title: SKMel5_IgG_SOX9_Myc_R1


title: SKMel5_H3K4me3_SOX9_Myc_R1


title: SKMel5_SOX9_SOX9_Myc_R1


title: H929 cells, IGF2BP1 knockdown, rep 3

city: Shanghai

first: Jiadai

state: Shanghai

address: Fenglin Road 180, Shanghai, China

department: Hematology

institute: Zhongshan Hospital, Fudan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low-quality reads were removed. Then clean reads were retained and mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: counts and fpkm

source_name: cell line

extract_protocol:
Following the manufacturer's instructions, we extracted total RNA with the EZ-press Kit for RNA Purification. NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) was used to purify RNA and evaluated quantification. The Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) was used to assess the RNA integrity.
Then the libraries were constructed using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 according to the manufacturer’s protocol.

value: cell line

value: multiple myeloma cells

value: IGF2BP1 knockdown


title: kogata2as_d4_RNAseq_r2

value: knockout GATA2AS on day 4


title: koctrl_d7_RNAseq_r1


title: H929 cells, IGF2BP1 knockdown, rep 2


title: A375_H3K4me3_No_tfn_R2

value: No-tfn


title: Kang-NT1

value: Liver hepatic stellate cells


title: H929 cells, IGF2BP1 knockdown, rep 1


title: SKMel5_HA_SOX9_HA_R1

value: Melanoma

value: HA


title: TGW, DMSO, SMAD4 ChIP, input

value: TGW

value: DMSO control


title: TGW, 3day 2uM ATRA, Replicate1, SMAD4 ChIP

value: 3 day 2uM ATRA


title: H929 cells, IGF2BP1 Negative Control, rep 3

value: IGF2BP1 NC


title: koctrl_d4_RNAseq_r2

value: knockout control on day 4


title: kogata2as_d4_RNAseq_r1


title: TGW, DMSO, Replicate1, SMAD4 ChIP

value: Neuroblastoma


title: TGW, 3day 0.5uM ATRA, RARA ChIP, input


title: SKMel5_SOX9_SOX9_HA_R1


title: SKMel5_SOX10_SOX9_HA_R1


title: koctrl_d4_RNAseq_r1


title: H929 cells, IGF2BP1 Negative Control, rep 2


title: H929 cells, IGF2BP1 Negative Control, rep 1


title: TGW, 3day 0.5uM ATRA, Replicate2, RARA ChIP


title: TGW, 1day 2uM ATRA, RARA ChIP, input

value: 1 day 2uM ATRA


title: SKMel5_H3K4me3_SOX9_HA_R1


title: kogata2as_d0_RNAseq_r2

value: knockout GATA2AS on day 0


title: SKMel5_SOX10_No_tfn_R1


title: koctrl_d0_RNAseq_r2

value: knockout control on day 0


title: SKMel5_IgG_SOX9_HA_R1

value: IgG


title: TGW, 3day 0.5uM ATRA, Replicate1, RARA ChIP


title: TGW, DMSO, Replicate2, SMAD4 ChIP


title: kogata2as_d0_RNAseq_r1


title: SKMel5_SOX9_No_tfn_R1


title: TGW, 1day 2uM ATRA, Replicate2, RARA ChIP


title: commissural neurons, rep 3

city: Montreal

first: Frederic

last: Charron

state: Quebec

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

data_processing:
Quality checking of read sequences was performed using FastQC. Adaptor sequences and low-quality score bases (Phred score < 30) were first trimmed using Trimmomatic v. 0.22, and reads less than 32-bp long were then discarded. The resulting reads were mapped to the rat genome (assembly rn6) using STAR.
Assembly: rn6
Supplementary files format and content: ens_allfpkm.csv: .CSV file type containing RNA-Seq FPKM for all 3 samples.

organism: Rattus norvegicus

source_name: spinal cord

growth_protocol: Commmissural neurons isolated from embryonic day 13 rat embryos were cultured for two days in vitro.

extract_protocol:
mRNA from dissociated commissural neurons was extracted with the RNAeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. RNA (350 ng to 1 mg) was incubated with 1 ml of 10x DNAse I buffer, 1 ml of DNAse I in 10 ml water for 15 mins at room temperature. DNAse digestion was stopped by addition of 1ml of Stop solution (containing EDTA) and incubation at 70C for 10 min.
cDNA libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). The resulting libraries were sequenced on the Illumina HiSeq2000 using 50 bp paired-end reads.

value: spinal cord

value: commissural neurons


title: koctrl_d0_RNAseq_r1


title: commissural neurons, rep 2


title: commissural neurons, rep 1


title: GATA2AS_ChIRP_even

data_processing:
For RNA-seq, Raw sequence reads were trimmed with cutadapt v3.4 to remove any adapters with trimming parameters "-a AGATCGGAAGAGCACACGT -q 20 --minimum-length=25". Trimmed reads were quantified with kallisto v0.46.2 with pre-built index of human Ensembl v96 transcriptomes provided by pachterlab github website. Differential expression was tested using R v4.1.0 with DESeq2 v1.32.0.  MA plot was produced with ggplot2. GO analysis was performed with clusterProfiler v4.0.5.
For ChIP-seq and ChIRP-seq, raw sequence reads were trimmed with cutadapt v3.4 with trimming parameters "-a CTGTCTCTTATACACATCT -q 20 --minimum-length=25". Trimmed reads were aligned with Bowtie2 v2.4.4 to pre-built human NCBI GRCh38 index provided by Bowtie website with parameter “--very-sensitive". Multimapping reads and duplicate reads were removed with sambamba v0.6.8 and picard v2.26.10. BigWig files were created with deepTools v3.5.1 using bamCoverage tool with the additional arguments “--binSize 10 --normalizeUsing CPM --extendReads 300”. Peaks were called for each replicate individually using macs v2.2.7.1. Conserved peaks were obtained from intersections between replicates by using BEDTools v2.30.0. Differential binding sites were obtained by DiffBind v3.2.7.
For ATAC-seq, Paired-end raw sequence reads were trimmed with cutadapt v3.4 with trimming parameters "-a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -q 20 --minimum-length=25". Trimmed reads were aligned with Bowtie2 v2.4.4 to pre-built human NCBI GRCh38 index provided by Bowtie website with parameter “--sensitive". Multimapping reads and duplicate reads were removed with sambamba v0.6.8 and picard v2.26.10. BigWig files were created with deepTools v3.5.1 using bamCoverage tool with the additional arguments “--binSize 10 --normalizeUsing CPM”. Peaks were called for each replicate individually using macs v2.2.7.1 with parameters “--nomodel --shift 100 --extsize 200”. Conserved peaks were obtained from intersections between replicates by using BEDTools v2.30.0. Differential binding sites were obtained by DiffBind v3.2.7.
Assembly: hg38
Supplementary files format and content: Csv files contain differential expressed genes from RNAseq results. Bed files contain differential binding sites.
Library strategy: ChIRP-Seq

value: wild type


title: SKMel5_IgG_No_tfn_R1

value: No-tfn


title: TGW, DMSO, RARA ChIP, input


title: SKMel5_H3K4me3_Notfn_R1


title: H_12h_rep2

city: 福州

first: Rong

middle: rong

last: Xue

state: 福建

address: 福建省福州市仓山区

institute: 福建农林大学

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were aligned to the rice reference genome sequence Nipponbare-Reference-IRGSP-1.0 using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called using MACS v2.1.0 with the significance cut-off p-value <=0.05
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

organism: Oryza sativa

source_name: Rice leaf

growth_protocol: The seedlings were transferred to a plastic pot (1-liter plastic cups) containing 1 L paddy soil for culture, and rice seedlings were grown in a greenhouse at 28°C in a 14/10-h light/dark cycle with 60% humidity.

extract_protocol:
Leaf nuclei were separated and ChIP was performed by CUT&Tag assay
ChIP-seq libraries were prepared according to Illumina TruePrep kit (Vazyme # TD202), 10 ng of DNA was used as starting material for ip samples. Libraries were amplified using 16-18 cycles on the thermocycler. Post amplification libraries were size selected at 300-500bp in length using Tapestation(Agilent Technologies). Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: developmental stage

value: seedlings

tag: age

value: 20 days

value: Rice leaf

value: Rice leaf cell

value: Spodoptera frugiperda

value: H3K9ac (Abcam,#ab10812)


title: H_12h_rep1

tag: chip antibody


title: TGW, DMSO, Replicate2, RARA ChIP

value: TGW

value: DMSO control


title: H_3h_rep2


title: GATA2AS_ChIRP_Input

tag: genotype


title: H_3h_rep1


title: TGW, DMSO, Replicate1, RARA ChIP

value: Neuroblastoma


title: CHP-134, 1day 2uM ATRA, SMAD4 ChIP, input

value: 1 day 2uM ATRA


title: YTK107-2-H3

city: Chuncheon

first: Junsoo

last: Oh

country: South Korea

institute: Kangwon National University

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, S. pombe spike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

source_name: Yeast cell

growth_protocol: All strains were grown in 200ml of YPD (Yeast extract Peptone Dextrose; 1% Yeast Extract, 2% Peptone, 2% Dextrose (Glucose)) at 30℃ until OD600 was 0.5-0.6

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies.
Libraries were prepared with NEBNext ChIP-Seq Library Kit following the manufacturer’s instruction.

value: Yeast cell

value: Anti-Histone H3 (Abcam, ab1791)

value: ard1 deletion


title: YTK107-1-H3


title: A375_SOX9_SOX9_Myc_R1

value: Melanoma


title: A375_IgG_SOX9_Myc_R1

value: IgG


title: CK_rep2

value: control


title: TGW, 1day 2uM ATRA, Replicate1, RARA ChIP


title: CK_rep1


title: YTK107-2-H3K4me2

value: Anti-dimethyl-Histone H3 (Lys4) (Merck, 07-030)


title: CHP-134, 1day 2uM ATRA, Replicate2, SMAD4 ChIP


title: A375_H3K4me3_SOX9_Myc_R1


title: Pfk_16h

city: Tianjin

first: Jianggang

last: Yang

address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Corynebacterium glutamicum ATCC 13032 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count(version 0.13.5).
Assembly: Corynebacterium glutamicum ATCC 13032 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000011325.1/)
Supplementary files format and content: tab-delimited text files including Reads count for each sample.

organism: Corynebacterium glutamicum

source_name: Corynebacterium glutamicum

growth_protocol: The precultured Corynebacterium glutamicum ATCC 13032 and ΔpfkA mutant were inoculated in 50 mL BHI medium containing glucose concentration of 10 g/L. Samples were collected at 4 h, 10 h and 16 h.

extract_protocol:
Cells were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Corynebacterium glutamicum

value: Pfk

tag: time point


title: YTK107-1-H3K4me2


title: GATA2AS_ChIRP_odd

value: wild type


title: CHP-134, 1day 2uM ATRA, Replicate1, SMAD4 ChIP


title: CHP-134, DMSO, SMAD4 ChIP, input


title: YTK107-2-H3K4me3

value: Anti-trimethyl-Histone H3 (Lys4) (Merck, 07-473)


title: A375_Myc_SOX9_Myc_R1

value: Myc


title: A375_HA_SOX9_HA_R1

value: HA


title: WT_16h

value: WT


title: A375_SOX10_SOX9_HA_R1


title: A375_SOX10_SOX9_Myc_R1


title: YTK107-1-H3K4me3


title: A375_SOX9_SOX9_HA_R1


title: WT_10h


title: 8-AG treated Fischer344 rat RPE/choroids-03

city: Pittsburgh

first: Yuanyuan

last: Chen

state: PA

address: 1622 Locust Street,

department: Ophthalmology

institute: University of Pittsburgh

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
gene expression level was estimated using RSEM v1.2.15
Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p<0.05 and more than 1.5 fold changes were considered differentially expressed.
Goseq was used to perform GO enrichment analysis and Kobas was used to perform the pathway analysis.
Assembly: Rnor_6.0
Supplementary files format and content: txt and csv files include raw counts of each sample.
Supplementary files format and content: txt and csv files include RPKM values of each sample.
Supplementary files format and content: txt and csv files include fold change, p values, FDR and RPKM values of each sample in two groups
Supplementary files format and content: excel files include the DEGs upreguated and downregulated between two groups.

source_name: RPE/choroids

growth_protocol: We obtained young and aged Fischer 344 rats from Char les River Laboratories and the National Institute on Aging [NIA]. All animals were housed under standard 12-h light/12-h dark conditions in the animal facility at University of Pittsburgh.

extract_protocol:
Each eye ball was opened by removing the cornea, iris and lens, and the neural retina was firstly isolated and put into RNAzol immediately and flash frozen in liquid nitrogen. After the neural retina being taken, RPE/choroids were isolated by washing the remaining eye cup with RNA zol and flash frozed in liquid nitrogen. Total RNA was isolated follwing manufacturer's instructions of RNAzol (Sigma-Aldrich, Saint-Louis, MO). Only samples with RNA integrity number (RIN) > 7 was selected for poly-A captured mRNA library preparation.
To compare old vs. young and 8-AG treated aged vs untreated aged neural retinae, mRNA libraries were prepared using poly-A capturation (N=3).  For RNA from RPE/choroids, due to low RNA yield,  mRNA lirbaries were genereated using polyA selection with enrichment for full-length transcripts.

treatment_protocol: We used four months adult rats as young control and aged rats at 22-24 months of age with or without 8-AG treatment. The 22 months old rats were treated with 8-AG (5 mg/kg body weight per day) daily by supplementing 8-AG in drinking water or water only for the untreated old group. Animals were treated for 8 weeks until they were 24 months of age and they were euthanized and eyes were enucleated immediately.

value: RPE/choroids

value: 8-AG treated old-24 months


title: A375_H3K4me3_SOX9_HA_R1


title: YF336-1-H3

value: Wildtype (BY4741)


title: 8-AG treated Fischer344 rat RPE/choroids-02


title: YF336-2-H3K4me2

value: Yeast cell


title: A375_SOX10_mCherry_R1

value: mCherry


title: 8-AG treated Fischer344 rat RPE/choroids-01


title: YF336-1-H3K4me2


title: CHP-134, DMSO, Replicate2, SMAD4 ChIP

value: Neuroblastoma

value: DMSO control


title: A375_SOX9_mCherry_R1

value: Melanoma


title: CHP-134, 3day 2uM ATRA, SMAD9 ChIP, input

value: 3 day 2uM ATRA


title: YF336-2-H3

value: Anti-Histone H3 (Abcam, ab1791)


title: Aged Fisher344 rat RPE/choroids-03

value: untreated old-24 months


title: A375_IgG_mCherry_R1

value: IgG


title: Aged Fisher344 rat RPE/choroids-02


title: CHP-134, 3day 2uM ATRA, Replicate2, SMAD9 ChIP


title: YF336-2-H3K4me3


title: CHP-134, 6day 2uM ATRA, Replicate1, SMAD9 ChIP

value: 6 day 2uM ATRA


title: YF336-1-H3K4me3

value: Anti-trimethyl-Histone H3 (Lys4) (Merck, 07-473)


title: CHP-134, 3day 2uM ATRA, Replicate1, SMAD9 ChIP


title: A375_H3K4me3_mCherry_R1


title: A375_IgG_SOX9_HA_R1


title: CHP-134, 6day 2uM ATRA, SMAD9 ChIP, input


title: CHP-134, 6day 2uM ATRA, Replicate2, SMAD9 ChIP


title: Aged Fisher344 rat RPE/choroids-01


title: A375_SOX10_No_tfn_R1

value: No-tfn


title: CHP-134, 1day 2uM ATRA, SMAD9 ChIP, input

value: 1 day 2uM ATRA


title: Young Fischer344 rat RPE/choroids-03

value: WT

value: untreated young-4 months


title: 232470

type: genomic

city: nice

first: Ilaria

last: Di Mauro

address: 28 avenue de valombrose

country: France

institute: CHU de Nice

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
primary data description: The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

label: Biotin

source_name: in situ melanoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).

value: in situ melanoma

tag: gender

value: female


title: 232469-1

tag: tissue


title: CHP-134, 1day 2uM ATRA, Replicate2, SMAD9 ChIP


title: A375_SOX9_No_tfn_R1

tag: antibody


title: 232385

source_name: invasive melanoma

value: invasive melanoma


title: 232086

value: male


title: CHP-134, 1day 2uM ATRA, Replicate1, SMAD9 ChIP

value: Neuroblastoma


title: Pfk_10h

value: Corynebacterium glutamicum

value: Pfk


title: Young Fischer344 rat RPE/choroids-01

value: RPE/choroids


title: CHP-134, DMSO, SMAD9 ChIP, input

value: DMSO control


title: CHP-134, DMSO, Replicate2, SMAD9 ChIP


title: Adipose_CD45positive_Tom_negative

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

description: 12X Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger package (version 3.0.2) was utilized to process unique molecular identifiers (UMIs) and barcodes and align the transcripts to a mm10 mouse reference genome, which was supplied with tdTomato and WPRE sequences manually.
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: Gonadal adipose tissue

extract_protocol:
Gonadal adipose tissue samples were subjected to direct mincing using a sharp scissor, followed by digestion in DMEM supplemented with 0.3 unit/ml Liberase TM (Roche) and 10% BSA at 37°C for 50 min with gentle shaking. After incubation, the resulting cell suspension was centrifuged at 400g for 3 min, and the supernatant was removed. The stromal vascular fractions (SVFs) present in the cell pellet were resuspended in DMEM and passed through 100 µm cell strainers. Subsequently, the red blood cells were lysed using RBC buffer for 5 min. The remaining cells were washed with PBS and resuspended in PBS containing 4% FBS and mouse FcR blocking reagent (MACS) at 4°C for 10 min, and further stained with anti-CD31antibodies and anti-CD45 antibody at 4°C for 30 min, washed and  passed through 70 µm cell strainers and then subjected to FACS SORP Aria (BD Biosciences) to sort out cells.The single-cell suspension of CD45- Tom+ cells,CD45- Tom- cells, CD45+ Tom+cells and CD45- Tom- cells were conducted to the sc-RNA seq sequencing.
For the scRNA-seq library construction, we followed the manufacturer’s instructions of 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1.

value: Gonadal adipose tissue

value: stromal vascular fractions

tag: group


title: Adipose_CD45positive_Tom_positive

description: 11X Genomics


title: A375_H3K4me3_No_tfn_R1

value: Melanoma

tag: date of sequencing

tag: round of transfection


title: 230874


title: SKMel5_SOX10_No_tfn_R0

tag: cell type

tag: treatment


title: 230873


title: SKMel5_SOX9_No_tfn_R0


title: Adipose_CD45negative_Tom_negative

description: 10X Genomics


title: CHP-134, DMSO, Replicate1, SMAD9 ChIP

tag: cell line


title: 230872


title: CHP-134, 1day 2uM ATRA, RARA ChIP, input


title: 230870


title: 230869


title: Young Fischer344 rat RPE/choroids-02


title: CHP-134, 1day 2uM ATRA, Replicate2, RARA ChIP


title: SKMel5_IgG_No_tfn_R0

value: IgG


title: SKMel5_H3K4me3_No_tfn_R0

value: No-tfn


title: Adipose_CD31negative_CD45negative_Tom_negative

description: 10X Genomics

extract_protocol:
Gonadal adipose tissue samples were subjected to direct mincing using a sharp scissor, followed by digestion in DMEM supplemented with 0.3 unit/ml Liberase TM (Roche) and 10% BSA at 37°C for 50 min with gentle shaking. After incubation, the resulting cell suspension was centrifuged at 400g for 3 min, and the supernatant was removed. The stromal vascular fractions (SVFs) present in the cell pellet were resuspended in DMEM and passed through 100 µm cell strainers. Subsequently, the red blood cells were lysed using RBC buffer for 5 min. The remaining cells were washed with PBS and resuspended in PBS containing 4% FBS and mouse FcR blocking reagent (MACS) at 4°C for 10 min, and further stained with anti-CD31antibodies and anti-CD45 antibody at 4°C for 30 min, washed and  passed through 70 µm cell strainers and then subjected to FACS SORP Aria (BD Biosciences) to sort out cells.The single-cell suspension of CD31- CD45- of Tom+ cells and Tom- cells were conducted to the sc-RNA seq sequencing.
For the scRNA-seq library construction, we followed the manufacturer’s instructions of 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1.

value: Adipocyte progenitor cells and Mesothelial cells


title: A375_IgG_No_tfn_R1


title: CHP-134, 1day 2uM ATRA, Replicate1, RARA ChIP

value: 1 day 2uM ATRA


title: 230868


title: Adipose_CD31negative_CD45negative_Tom_positive

description: 10X Genomics


title: A375_SOX9_No_tfn_R0


title: A375_IgG_No_tfn_R0


title: 230867


title: 230633-2


title: CHP-134, DMSO, RARA ChIP, input


title: A375_SOX10_No_tfn_R0


title: Adipose_CD45negative_Tom_positive

description: 10X Genomics


title: A375_H3K4me3_No_tfn_R0


title: 230633-1


title: Fetal liver HSPC, infected with MLLT3-S-OE vector sample6

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

description:
MLLT3-S_OE_4w_HSPC_6
human FL CD34+CD38-/lowCD90+GFP+

data_processing:
Alignment: TopHat v2.0.14, parameters --no-coverage-search --library-type fr-firststrand -o
Coverage file: Genomecov, Bedtools, parameters -bg -split –ibam
Tags: Maketagdirectory
RPKM: analyzeRepeats.pl, parameters -rna hg19 -noadj or -rpkm -strand - -count exons -condenseGenes
DGE: getDiffExpression.pl
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing RPKM and DGE.

source_name: FL CD34+CD38-/lowCD90+GFP+

growth_protocol: Fetal Liver is mechanically disrupted. CD34+ cells are magnetically separated. The indicated phenotype are FACS sorted.

extract_protocol:
Cells are FACS sorted in RLT and RNA is extracted using RNeasy Mini kit (Qiagen).
KAPA RNA HyperPrep Kit with RiboErase (HMR).

treatment_protocol: Cells are infected with CTR or MLLT3-OE virus and cultured on OP9M2 stroma.

value: FL CD34+CD38-/lowCD90+GFP+

value: Infected with MLLT3-S-OE vector

tag: time


title: H929 cells, m6a-seq, Input

data_processing:
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Then randomly extract 250 thousand paired reads from clean data, use the blastn software to alignment with the NT database (ftp://ftp.ncbi.nih.gov/blast/db). And take the best result with evalue < 1e-10 and coverage > 80%.
Use the SortMeRNA software for ribosomal RNA reads removal. After discarded the rRNA reads, the remainly clean reads were mapped to the reference genome using HISAT2 with default parameters. Unique reads with high mapping quality were retained.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: m6a-seq

extract_protocol:
Cells lysis was performed in cold wash buffer (50mM Tris 7.4, 150mM NaCl, 2mM EDTA, 0.1% SDS, 0.5% NP-40, and 0.5% deoxycholate) supplemented with a 1% RNase inhibitor (Takara) and 2% protease inhibitor cocktail (Roche) for 30 min.After Ip,the protein-RNA complexes were cut from the gel and RNA was extracted with Trizol after digesting the proteins.
cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) according the manufacturer’s procedure.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq 6000 system for 150 nt paired-end sequencing.

value: cell line

value: m6a input


title: Fetal liver HSPC, infected with MLLT3-S-OE vector sample5

description:
MLLT3-S_OE_4w_HSPC_5
human FL CD34+CD38-/lowCD90+GFP+


title: tissue, MC_2, Disease group

city: Kaifeng

first: zhao

last: qingchun

address: North section of Jinming Avenue, Kaifeng City, Henan Province

institute: National R&D Center for Edible Fungus Processing Technology

data_processing:
The raw data obtained by sequencing was filtered using the filtering software SOAPnuke (v1.6.5)
Assembly: NCBI_GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Splenic organ

extract_protocol:
Appropriate amount of tissue samples were taken, 1.5mL of TRIzol lysate was added, and put into a tissue grinder for 30s grinding, and then removed and left for 5min to fully lysate the tissue cells.The ground and crushed tissue samples were centrifuged, and the supernatant was transferred into an EP tube filled with 300µL chloroform/isoamyl alcohol (24:1). The supernatant was absorbed into a new 1.5 mL centrifuge tube, and dissolved and precipitated with 20-200 µL DEPC water or RNase-free water.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.The PCR reaction system and program are configured and set up to amplify the product.The corresponding library quality control protocol will be selected depending upon product requirements.Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.

value: Splenic organ

value: Disease group

value: immunosuppression


title: tissue, MC_3, Disease group


title: tissue, MD_3, Disease group and AVFP therapy

value: Disease group and AVFP therapy


title: tissue, MD_2, Disease group and AVFP therapy


title: CHP-134, DMSO, Replicate1, RARA ChIP

value: Neuroblastoma


title: tissue, MD_1, Disease group and AVFP therapy


title: H929 cells, IGF2BP1 Clip-seq Input, rep 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. Then randomly extract 250 thousand paired reads from clean data, use the blastn software to alignment with the NT database (ftp://ftp.ncbi.nih.gov/blast/db). And take the best result with evalue < 1e-10 and coverage > 80%.
Use the SortMeRNA software for ribosomal RNA reads removal. After discarded the rRNA reads, the remainly clean reads were mapped to the reference genome using HISAT2 with default parameters. Unique reads with high mapping quality were retained.
Assembly: hg38
Supplementary files format and content: bigWig

value: IGF2BP1 clip Input


title: Fetal liver HSPC, infected with MLLT3-OE vector sample6

value: Infected with MLLT3-OE vector


title: tissue, MC_1, Disease group


title: CHP-134, DMSO, Replicate2, RARA ChIP

value: DMSO control


title: Fetal liver HSPC, infected with MLLT3-OE vector sample5


title: tissue, BC_3, Blank control

value: Blank control


title: H929 cells, IGF2BP1 Clip-seq IP, rep 2

value: IGF2BP1 clip IP, Novus:NBP1-79024


title: H929 cells, IGF2BP1 Clip-seq Input, rep 1


title: tissue, BC_2, Blank control


title: Fetal liver HSPC, infected with CTR FUGW vector sample6

value: Infected with CTR FUGW vector


title: 230631

value: invasive melanoma

value: female


title: H929 cells, m6a-seq, IP

value: m6a ip, Synaptic Systems, 202 003


title: tissue, BC_1, Blank control


title: Fetal liver HSPC, infected with CTR FUGW vector sample5

value: FL CD34+CD38-/lowCD90+GFP+


title: WT_LCL_Rep1

status: Public on May 30 2024

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Aligned to Grch38 using Hisat2 to generate sam files
Sam files were sorted and converted to bam files using samtools
Read counts were extracted using featureCounts
Assembly: GRCh38/hg38
Supplementary files format and content: tab delimited text file containing raw counts from each sample

source_name: LCL

extract_protocol:
RNA was extracted using mini Rneasy kit (Qiagen 74104) including on-column DNase digestion
PolyA mRNA (E7490S) was isolated and libraries were made with the NEBNext Ultra II RNA Library Prep kit (E770S) and indexed (E7500S) following manufacturer's protocol.

tag: donor

value: LCL

value: WT


title: LPKO_LCL_Rep1

value: LPKO


title: LPKO_LCL_Rep3


title: WT_LCL_Rep3


title: WT_LCL_Rep2


title: LPKO_LCL_Re2


title: Hematopoetic_CD8T_63

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

data_processing:
The resulting read count matrix was passed through robust QC procedure to remove ROIs of low surface area (<5000 µm2) or low perfect aligned reads (< 80%), and probes of low quality or identified as global or local outliers (fails Grubbs outlier test in ≥ 20% segments). Genes differentially expressed between groups of interest were detected using gene-wise linear modeling in R (limma, v3.50.3), with p-value adjusted for false discovery rate.
FASTQ files were decoded using a Nanostring  GeoMx NGS pipeline app version 2.0.21
Assembly: HGR38
Supplementary files format and content: normalized matrix count
Library strategy: Spatial Transcriptomics

source_name: synovium

growth_protocol: Back paws were decalcified in 14% of EDTA for two weeks before being embedded in paraffin. Then,  4 um-thick  parafin sections were stained with human anti CD45 and Human anti CD8 T cells. Stained slides were loaded and scanned onto a GeoMx instrument.

extract_protocol:
Stained slides were loaded and scanned onto a GeoMx instrument.Seven Regions of interest (ROI) were selected based on the CD45 and CD8 fluorescent staining and auto-segmentation algorithm. RNA was isolated using Agilent RNA isolation kit with manufactured recommended protocol.
Photocleaved oligonucleotides from the ROI were collected and products were processed and sequenced on an Illumina NextSeq 2000. The ROI were selected based on the positive staining of CD8 and CD45

treatment_protocol: The slides were processedfollowing the NanoString protocols as documented in Manual Slide Preparation MAN-10150-01.The slides were stained with antibodies specific for human anti-CD8 (EPR21769, AbCam) and anti-CD45 (EM-05, Novus).

value: synovium

value: Hematopoietic cells (CD45+/CD8+/CD8-)

tag: roi lot

value: collect slide 7

tag: condition

value: Ps


title: Hematopoetic_CD8T_66


title: Hematopoetic_CD8T_61


title: Hematopoetic_CD8T_65


title: Hematopoetic_CD8T_62


title: Hematopoetic_CD8T_64


title: Hematopoetic_CD8T_60


title: Hematopoetic_CD8T_59


title: H929 cells, IGF2BP1 Clip-seq IP, rep 1

value: cell line


title: Hematopoetic_CD8T_58


title: Hematopoetic_CD8T_55


title: Hematopoetic_CD8T_54


title: Hematopoetic_CD8T_56


title: Hematopoetic_CD8T_53


title: Hematopoetic_CD8T_57


title: Hematopoetic_CD8T_18

value: collect slide 6


title: Hematopoetic_CD8T_17


title: Hematopoetic_CD8T_16


title: Hematopoetic_CD8T_10


title: Hematopoetic_CD8T_51


title: Hematopoetic_CD8T_15


title: Hematopoetic_CD8T_12


title: Hematopoetic_CD8T_8


title: Hematopoetic_CD8T_11


title: Hematopoetic_CD8T_9


title: Hematopoetic_CD8T_6


title: Hematopoetic_CD8T_7


title: Hematopoetic_CD8T_52


title: Hematopoetic_CD8T_14


title: Hematopoetic_CD8T_5


title: Hematopoetic_CD8T_4


title: Hematopoetic_CD8T_2


title: Hematopoetic_CD8T_3


title: Hematopoetic_CD8T_95

value: collect slide 4

value: PsA


title: Hematopoetic_CD8T_1


title: CHP-134, DMSO, Replicate1, SMAD4 ChIP

data_processing:
bcl2fastq v2.20.0.422 was applied for converting per-cycle BCL basecall files to per-read fastq files
trimgalore v0.4.4 was applied to remove low quality reads and adaptor with default setting
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA mem v0.7.17 with default setting
To generate genome-wide coverage profiles, the bedtools v2.17.0 “genomecov” command was applied , and the output was converted to bigwig files using bedGraphToBigWig
MACS2 v2.1.1 was utilized to identify ChIP-seq signal enriched regions (narrow peaks) with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: BigWig, narrowPeak(except for input sample)

value: Neuroblastoma

value: DMSO control


title: 230595

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

source_name: sarcoma

value: male

tag: tumor stage

value: grade 2


title: Hematopoetic_CD8T_94


title: Hematopoetic_CD8T_92


title: Hematopoetic_CD8T_90


title: Hematopoetic_CD8T_88


title: Hematopoetic_CD8T_89


title: Hematopoetic_CD8T_93


title: Hematopoetic_CD8T_87


title: Hematopoetic_CD8T_91


title: Hematopoetic_CD8T_82


title: Hematopoetic_CD8T_86


title: Hematopoetic_CD8T_85


title: Hematopoetic_CD8T_84


title: Hematopoetic_CD8T_49

value: collect slide 3


title: Hematopoetic_CD8T_48


title: Hematopoetic_CD8T_47


title: Hematopoetic_CD8T_50


title: 214110


title: 212682


title: Hematopoetic_CD8T_83


title: 200850


title: Hematopoetic_CD8T_46


title: Hematopoetic_CD8T_45


title: Hematopoetic_CD8T_44


title: Hematopoetic_CD8T_42


title: 231240


title: Hematopoetic_CD8T_41


title: Hematopoetic_CD8T_43


title: Hematopoetic_CD8T_40


title: Hematopoetic_CD8T_39


title: Hematopoetic_CD8T_38